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After an election, the West African nation starts to recover from a year of political instability

As U.S. drones continue to rain Hellfire missiles down from the Yemen sky, another region of the world is undergoing a transition that could have a significant impact on how America approaches its counter-terrorism policies in the coming years. The citizens of Mali elected ex-Prime Minister Ibrahim Boubacar Keita as their next president in a run-off vote earlier this week, defeating his long-time political rival, Soumaila Cisse, a former finance minister. The election will unlock $4 billion in foreign aid, and was praised by international observers. It comes after a year of massive instability in that country, including a coup by U.S.-trained Malian military members and a rebellion in the North that resulted in a French-led intervention to defeat an alliance between Tuaregs – a separatist ethnic group in the North – and al Qaeda in the Islamic Maghreb (AQIM), one of several Islamist groups in the region.

Prior to the coup, the U.S. military had trained members of Mali's security forces as part of a wider counter-terrorism training operation in West Africa. The first iteration of that program, announced in 2002, was called the Pan-Sahel Initiative, and included Mali, Niger, Chad and Mauritania. "Since then, three of the four militaries have staged coups," says Michael McGovern, a political anthropologist who specializes in West Africa. He stresses that correlation doesn't equal causation, and that "the coups may have happened without U.S. involvement."

The military takeover in Mali triggered what's known as the Leahy amendment, which, among other things, prohibits the U.S. from providing military training to governments that have come to power in a coup. That meant the U.S. military officially had to leave the country – although a car accident on Martyrs Bridge involving three special operations forces showed that at least a small U.S. presence stayed behind.

Now, however, the election likely means that U.S. training in Mali will resume. "Following the return of a democratically-elected government to office, the United States will seek to normalize its foreign assistance to Mali," says Will Stevens, spokesperson for Africa Affairs at the State Department. "Our assistance programs will be reviewed and revised to address the security and development needs of the country in light of the new environment." A spokesperson for the Pentagon said that once the State Department opens the door for the U.S. military to re-engage, it will do so. "We're eager to resume the relationship," says Air Force Major Rob Firman. The Pentagon recently announced it was looking for instructors in the Tuareg language.

The new Malian government will face many of the same problems that led to the northern rebellion in 2012. "While the elections went about as well as they possibly could have, there is no question that northerners (especially Tuaregs) basically did not participate," says McGovern. "This makes the task of the next president in building legitimacy in the very zones from which the problems emerged that much harder. Consequently, it is all too easy to see the possibility of new separatist insurgencies popping up again in another two or three years." (Mali's U.S. embassy did not respond to a request for comment for this story.)

Will al Qaeda continue to make common cause with the Tuareg separatists in the north? McGovern believes it's possible, although he notes that last year's alliance actually left the separatists worse off: "They've been painted with the stain" of jihadism, he says.

The conventional wisdom on AQIM sees them as primarily a regional threat, though some disagree with that assessment. Daveed Gartenstein-Ross, a senior fellow at the Foundation for Defense of Democracies, believes there is some evidence that AQIM "has previously played a role in plots beyond the region." He cites a letter obtained by U.S. special forces after the raid on Osama bin Laden's Abbottabad compound that directs a top al Qaeda operative to include AQIM in planning and financial support of an eventual plot to bomb European cities. "There are a whole lot of unknowns related to this particular piece of evidence, so I don't want to claim any false certainty," says Gartenstein-Ross. "But, to me, the likelihood is that AQIM was involved in a plot beyond the immediate region at bin Laden's request."

Gartenstein-Ross adds that he thinks U.S. training of Malian forces will, and should, resume, and that a U.S. presence can help mitigate – though not eliminate – some of the abuses the Malian military has engaged in. "Whether training missions end up being a net positive ultimately depends upon the efficacy of the training provided," he says. "U.S.-provided [counter-terrorism] training has a mixed record, and it is important to carefully monitor which training, and which departments of the U.S. government, achieve positive results, and which ones consistently fall short."

Marla Keenan, the director of military engagement at the Center for Civilians in Conflict, believes that if training resumes, U.S. forces need to make civilian protection a top priority for the Malian military. "Over the last year, Malians have faced death, injuries, looting, displacement, fear," she says. "The last thing they need is a military accidentally harming the people while trying to keep the peace. "Understanding the importance of civilian protection is not as easy as teaching someone how to shoot straight but it's just important, if not more so."

If training does resume, Corinne Dufka, senior researcher on West Africa at Human Rights Watch, says one of the primary focuses must be on rooting out entrenched corruption and investigating prior human rights abuses. "I have documented, for example, about 25 summary executions, 11 disappearances and over 100 cases of very serious abuse and torture," Dufka says. "The U.S. government must insist on investigations and that those implicated are held accountable lest the incidents become a well entrenched pattern."

One of those implicated in alleged human rights abuses – including "arbitrary detention, enforced disappearances, attacks against journalists and torture," according to Dufka – is Amadou Sanogo, the leader of the coup, who was recently promoted from captain to general, skipping several ranks. Dufka calls the move "outrageous," and adds that "instead of being rewarded with this promotion, Sanogo should have been investigated for his alleged involvement in these acts."